To investigate major factors controlling variations in water quality, principal component analysis and cluster analysis were used to analyze data sets of 12 parameters measured at 23 sampling stations of Jinhae Bay during winter and spring. Principal component analysis extracted three major factors controlling variations of water quality during winter and spring. In winter, major factors included freshwater input, polluted material input, and biological activity. Whereas in spring they were polluted material input, freshwater input, and suspended material input. The most distinct difference in the controlling factors between winter and spring was that the freshwater input was more important than the polluted material input in winter, but the polluted material input was more important than the freshwater input in spring. Cluster analysis grouped 23 sampling stations into four clusters in winter and five clusters in spring respectively. In winter, the four clusters were A (station 5), B (stations 1, 2), C (station 4), and D (the remaining stations). In spring, the five clusters included A (station 5), B (station 1), C (station 3), D (station 6), and E (the remaining stations). Intensive management of the water quality of Masan and Hangam bays could improve the water quality of Jinhae Bay since the polluted materials were mainly introduced into Jinhae Bay through Masan and Hangam bays.